Now, in Prometheus, some of the fauna seems to correspond to what we know about Xenemorphic physiology, but some of it seems to work differently. In place of eggs, at this stage, there are what appear to be graphite cylinders, doubtless of industrial manufacture. There is living tissue within. Where does that tissue come from? There is no Queen around, and if there were, she presumably wouldn't lay graphite tubes. So perhaps the genetic material is entirely engineered. That's fine, but at what stage were egg-laying Queens developed? It doesn't seem credible that the engineers would have designed them, because a Queen is inevitably an extremely powerful, dangerous and independent creature who would likely be impossible to control, and whose brood would likely be impossible to contain. So did Queens evolve? I don't see how. Gender differentiation must occur the very early stages of the evolutionary tree (premammalian in our case), so I don't see how it could have developed once the Xenomorphs were established as bipedal vertebrates, no matter how much they changed otherwise. Even it was possible, it would require millions of years, especially since the Xenemorphs' birth and death rate is very low at this stage. I can't understand this at all.
Secondly, how does the genetic material in the cylinders behave? It appears to be a inanimate ooze when David first investigates it. But there are "worms" on the ground. How do the two relate? When the lost astronauts return to the chamber, they are attacked and killed by serpentine beings of considerable strength and ferocity. Are these supposed to have "hatched" from the cylinders, or are they the "worms", having undergone a vastly accelerated growth?
The latter seems more likely given the fate of Holloway. David tricks him into ingesting the "ooze" from a cylinder. He then seems to mutate into a hyper-aggressive, super-strong monster who is almost invulnerable. Did the same thing happen to Holloway as happened to the "worms"?
That would be fairly satisfactory- the engineers' biological weapon is an "ooze" that effectively "weaponises" any lifeforms on which they care to use it. But how, then, do we explain Shaw's freak pregnancy, and the physiology of the creature that grows within her? Holloway was undergoing a transformation when the two had sex, and the insinuation is clearly that the creature was transmitted to Shaw in Holloway's sperm. Was the creature a super-mutated sperm, effected by the "ooze"? That doesn't seem likely, because its physiology was too complex. It had too many tentacles, and gnashing mouths. So, it has to be an "original" alien creature. So, were the cylinders supposed to be carrying the seed of these squid-like creatures? If so, are we supposed to believe that the "weaponising ooze" is relatively incidental, like an egg-white to its yolk? That doesn't seem credible, since the effects of the ooze are so dramatic, and David clearly has ideas about what to do with it.
And how are these squid creatures usually born? It seems impractical for them to rely on being ingested and then planted inside another creature's womb. And why were the "worm/serpents" so keen to get inside peoples' throats? Presumably to get access to their gastric tracts, were they could either gestate or lay eggs to incubate. So, we're returning to the idea that the "squids" are usually born when the "serpents" impregnate a victim. Where the "worms" just "worms" then, independent of the "serpents"? Or where they indeed one and the same, and just a minor alien species that happened to be effected by the "weaponising ooze"? I actually like that, because it ultimately preserves the idea that the Xenomorphs are primarily a product of nature rather than design.
The problem with it, however, is the worm/serpent/squid/Xenomorph lifecycle. Unlike the facehugger from "Alien" and "Aliens", which simply looks to feed and reproduce once it has burst from a human victim as a fully formed adolescent Xenomorph, the "squid" seeks to impregnate another being again. Despite its enormous size and strength, its immediate priority when it meets with the engineer is to thrust its sex organs into his (?) throat, and impregnate him with a version of the Xenomorph we know. Several questions are raised by this. Firstly, why isn't the enormous and powerful "supersquid" the finished article? Secondly, why is its offspring so obviously physiologically different? I can accept "worm" > "serpent" and even "worm" > "serpent" > "squid" > "supersquid", but how can it be "worm" > "serpent" > "squid" > "supersquid" > "biped vertebrate with exoskeleton"? The last part just doesn't ring true, since the "proto-Xenomorph" doesn't resemble and of the previous stages in its life cycle at all. The Xenomorph does look a bit like the facehugger that creates it in "Alien", but its inception by the "supersquid" seems highly implausible. Finally, why would a species have three stages of generation (birth, metamorphosis to squid, metamorphosis to Xenomorph)? It seems contrived and I can't imagine an evolutionary basis for it, particularly since a stage has been shed by the time we meet these creatures in "Alien", just thirty years later.
So, I cannot come up with a coherent theory that explains the ooze and its effects, the lack of a Queen, the worms, the serpents, the life cycle of the squid; and how all of these refine themselves to create the Xenomophs, who have a clear and understandable reproduction based on Queens and eggs, and a clear one-stage metamorphosis from face-hugger to adult.
Your thoughts please!